expair Class Reference

List of all members.

Public Member Functions
	expair (int i1, int i2, int a1=0, int a2=0)
	expair (int i1, int i2, int a1, int a2, int ms)
int	matchState () const
bool	isStart () const
int	extra1 () const
int	extra2 () const
int	index1 () const
int	index2 () const
int	endIndex1 () const
int	endIndex2 () const
Public Attributes
int	idx1
int	idx2
int	ia1
int	ia2
int	exms

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Constructor & Destructor Documentation

expair::expair	(	int	i1,
		int	i2,
		int	a1 = 0,
		int	a2 = 0
	)			[inline]

expair::expair	(	int	i1,
		int	i2,
		int	a1,
		int	a2,
		int	ms
	)			[inline]

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Member Function Documentation

int expair::matchState

(

)

const [inline]

References exms.

bool expair::isStart

(

)

const [inline]

References idx1, and idx2.

int expair::extra1

(

)

const [inline]

References ia1.

int expair::extra2

(

)

const [inline]

References ia2.

int expair::index1

(

)

const [inline]

References idx1.

int expair::index2

(

)

const [inline]

References idx2.

int expair::endIndex1

(

)

const [inline]

References ia1, and idx1.

int expair::endIndex2

(

)

const [inline]

References ia2, and idx2.

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Member Data Documentation

int expair::idx1

index of the two input vectir<int>

Referenced by endIndex1(), index1(), and isStart().

int expair::idx2

Referenced by endIndex2(), index2(), and isStart().

int expair::ia1

right now I am only testing only one intron loss

Referenced by endIndex1(), and extra1().

int expair::ia2

Referenced by endIndex2(), and extra2().

int expair::exms

match state, right now 0 exact match, 1 mismatch small difference of internal exons, slightly larger difference of end exons. Should differ by a multiple of 3. 2 insert or deletion of intron 3 4 end of exon indel + small difference (abs(diff)<30) Should not record end state in this variable. A simple comparison is enough.

Referenced by matchState().

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The documentation for this class was generated from the following file:

• seqaln/src/alnexon.cpp